LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 250 butane system for drude polarizability example (Langevin)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5

pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.butane
  orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  4500 atoms
  scanning bonds ...
  5 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  9 = max dihedrals/atom
  reading bonds ...
  4250 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6750 dihedrals
  5 = max # of 1-2 neighbors
  8 = max # of 1-3 neighbors
  12 = max # of 1-4 neighbors
  17 = max # of special neighbors

comm_modify vel yes

group gBUTANE molecule 1:250
4500 atoms in group gBUTANE
group gCORES type 1 2 3
3500 atoms in group gCORES
group gDRUDES type 4 5
1000 atoms in group gDRUDES

pair_coeff    1    1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H
pair_coeff    1    2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H
pair_coeff    1    3 lj/cut/coul/long 0.044496 2.958040 # C3H H
pair_coeff    2    2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H
pair_coeff    2    3 lj/cut/coul/long 0.044496 2.958040 # C2H H
pair_coeff    3    3 lj/cut/coul/long 0.029999 2.500000 # H H
pair_coeff    *  4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff    1    * thole 1.368000
pair_coeff    2    * thole 1.368000
pair_coeff    4    * thole 1.368000
pair_coeff    5    * thole 1.368000

neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C N D D

fix fSHAKE gCORES shake 0.0001 20 0 b 2 4
  0 = # of size 2 clusters
  500 = # of size 3 clusters
  500 = # of size 4 clusters
  0 = # of frozen angles

fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
fix fNPH all nve

compute cTEMP all temp/drude

thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.367867
  grid = 36 36 36
  stencil order = 5
  estimated absolute RMS force accuracy = 0.031354
  estimated relative force accuracy = 9.44215e-05
  using double precision FFTs
  3d grid and FFT values/proc = 26875 11664
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 17
New max number of 1-2 to 1-4 neighbors: 17 (+0)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
  (2) pair thole, perpetual, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 16.75 | 17.03 | 17.13 Mbytes
Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
       0            0    6535.5187      2714.74    248.45112    3820.7787    3724.3278    140.75328    1.4735401            0   -518.77975    595169.42   -594696.41    4439.7916    55742.797    334.61375    18.435655 
      50   0.60067916    3418.0026    2021.3092    184.98882    1396.6934    835.43668     808.1357     113.8069            0   -759.89265    595242.48   -594843.28    3040.8412    55742.797    197.07838    152.67751 
     100    1.1808443    2892.8432    1932.7674    176.88554    960.07578    363.31823    924.84568    164.52097            0   -931.84989    595306.29   -594867.05    1694.4336    55742.797    224.44681     49.87859 
     150    1.7504072    2833.9225    1947.7257     178.2545    886.19681    243.64601    972.03324    186.73658            0   -941.85405    595295.47   -594869.83     4603.775    55742.797    239.63159     14.40403 
     200    2.3280952    2870.6299    1920.2424    175.73925    950.38759     226.3737    1061.7175    186.27763            0   -950.17253    595296.43   -594870.24    2606.5041    55742.797    239.64552    5.1468097 
     250    2.9009523    2894.0913     1933.574    176.95936    960.51728    215.18824    1118.0957    195.43563            0   -993.95102    595296.54    -594870.8    1812.6379    55742.797    242.26101    2.6446653 
     300    3.4866827    2959.1219    1970.1936    180.31075    988.92834    209.63552    1155.4811    193.64322            0    -996.9511    595297.92    -594870.8    3371.5528    55742.797    247.17325    1.8304564 
     350    4.1206505    2988.7765    1988.8664    182.01968    999.91007    217.65998    1148.4029    204.96757            0    -996.5586    595296.05   -594870.61    3021.4005    55742.797    249.63956    1.5179762 
     400    4.7467482    3014.5638    1983.6589    181.54309    1030.9049    225.81008    1174.5083    214.70193            0    -1012.492    595298.89   -594870.51    668.28879    55742.797    249.02834      1.40089 
     450    5.3385043     3065.528    2028.5299    185.64965    1036.9981    206.85828     1232.536     204.7453            0   -1034.5447    595297.52   -594870.12     1276.895    55742.797    254.65283    1.4568976 
     500    5.8841732    3087.3359    1998.9143    182.93925    1088.4216    209.84037    1244.2781    211.45124            0   -1004.5214     595297.9   -594870.53    1811.1357    55742.797    250.95893    1.3696214 
     550     6.495003    3082.7524     2000.662     183.0992    1082.0904    218.46927    1229.7948    204.12764            0   -997.16039    595297.23   -594870.37    2005.0512    55742.797    251.16775     1.399994 
     600    7.0529547    3089.1148    2008.9702    183.85957    1080.1445    215.63956    1239.6501     205.6559            0   -1008.3414    595297.61   -594870.07    1579.3906    55742.797    252.19307     1.453043 
     650    7.6147993    3094.7607     1984.215    181.59398    1110.5457     217.2587    1270.5436    217.11567            0   -1021.7236    595297.37   -594870.02    922.17911    55742.797    249.09972    1.3970954 
     700    8.1847589    3085.7974    1977.7443    181.00179    1108.0531    226.89107    1263.0937    209.93619            0   -1019.8382    595298.21   -594870.24    1358.6744    55742.797    248.27153    1.4348071 
     750    8.7551639    3098.7075    1990.5214    182.17114     1108.186    210.53964    1263.8112    208.67005            0   -1002.6807    595298.31   -594870.47    1389.4827    55742.797    249.86686    1.4670711 
     800    9.3312614    3106.7743    2001.1286    183.14191    1105.6457    223.39008    1267.3688    200.94765            0   -1014.1025     595298.4   -594870.36    498.96153    55742.797    251.20537    1.4561965 
     850    9.9120548    3162.1905    2015.7594     184.4809    1146.4311    238.91403    1296.3319    216.49567            0   -1033.2993    595298.07   -594870.08   -146.24973    55742.797    253.06241    1.4124079 
     900    10.506582    3151.6622    2017.7351    184.66172    1133.9272    225.66798    1259.6857    214.41352            0   -993.82625    595298.42   -594870.44    855.52595    55742.797    253.32946    1.3630807 
     950    11.073148    3108.5571    1984.4638    181.61676    1124.0933    219.09683    1258.9728     215.5009            0   -998.11162     595299.1   -594870.46    742.29532    55742.797    249.13228    1.3937456 
    1000    11.712476    3151.1431    2010.1073    183.96363    1141.0358    234.62673    1262.3296      218.152            0   -1001.9319    595297.94   -594870.08   -15.429859    55742.797    252.31702    1.5039719 
    1050    12.416933    3154.9906    2025.2409    185.34864    1129.7498    240.28475    1245.2732    211.12104            0   -994.07995    595297.56   -594870.41    220.34341    55742.797    254.21036    1.5313366 
    1100    13.000971    3146.7058    2015.0512    184.41609    1131.6546    217.69098     1255.773    216.52818            0    -985.5434    595297.52   -594870.32    245.54987    55742.797     252.9731    1.4117211 
    1150    13.566174    3184.3315    2097.0388    191.91954    1087.2926    210.06417    1226.6616    216.15719            0   -994.73562    595299.65   -594870.51     960.8241    55742.797    263.29333    1.3975188 
    1200    14.098352    3181.1191    2062.3454    188.74443    1118.7737    228.90526    1255.3357    202.92363            0   -997.73355    595299.52   -594870.18    341.31357    55742.797    258.91222    1.4415835 
    1250    14.653097    3174.3638    2030.9146     185.8679    1143.4492    239.32477    1267.7689    201.40964            0   -992.67835    595297.78   -594870.16    399.69023    55742.797    254.97189    1.4037218 
    1300    15.198202    3181.4157    2020.4604    184.91114    1160.9553    213.94195    1283.8134    212.79399            0   -977.52401    595298.12   -594870.19    141.81633    55742.797    253.64065     1.447907 
    1350    15.763844    3221.4526    2077.8786    190.16601     1143.574    237.97099    1261.8854    206.43835            0   -991.01514    595298.43   -594870.14    293.86155    55742.797    260.85797    1.4643006 
    1400     16.36341    3273.4082    2117.3713    193.78035    1156.0369    241.63847    1257.3077    215.03947            0   -986.42491     595298.6   -594870.13    881.28305    55742.797    265.82788    1.4598428 
    1450    16.907335    3277.2159    2086.1619    190.92409     1191.054    245.42292    1289.0177    220.33432            0   -991.71405    595297.92   -594869.93    24.577369    55742.797    261.91752    1.4173689 
    1500    17.461373    3277.8652    2139.2814    195.78556    1138.5838    230.79453    1253.5268     210.7018            0   -984.94169    595298.66   -594870.16    612.24618    55742.797    268.59444     1.432741 
    1550    17.996041    3247.9903    2120.4397    194.06118    1127.5505    237.85251    1244.2413    207.38138            0   -989.02975    595297.17   -594870.07    908.40409    55742.797    266.20105    1.4941148 
    1600    18.546506    3263.2065    2095.2604    191.75678    1167.9461    222.27478    1287.0828    217.80256            0   -988.01164    595299.17   -594870.37    372.09439    55742.797    263.06244    1.4165997 
    1650    19.087156     3279.007    2102.6708    192.43497    1176.3363    228.35925     1287.432    218.78886            0   -987.87117    595299.94   -594870.32   -277.43091    55742.797     263.9961    1.4129192 
    1700    19.665064    3297.4084    2103.7436    192.53316    1193.6648    248.40926    1304.8649    202.53258            0    -989.5236    595297.12   -594869.74    1158.9952    55742.797    264.11122    1.4655993 
    1750    20.367483    3280.0391    2075.6964     189.9663    1204.3427    240.06411    1311.9499    213.18798            0   -987.79028     595296.5   -594869.56    437.83034    55742.797    260.60055    1.4183112 
    1800    20.942509    3272.2429    2082.8406    190.62013    1189.4023    235.68331    1306.7318    216.11438            0   -997.06553    595297.79   -594869.86    1293.8956    55742.797    261.49937    1.4181999 
    1850    21.546463    3288.8649    2088.0429    191.09624     1200.822    239.22801    1297.8732    214.15066            0   -979.04152    595298.01   -594869.39    217.43385    55742.797    262.15237    1.4245994 
    1900    22.118972    3213.0018     2032.382    186.00219    1180.6198    222.35796    1278.9261    222.52754            0    -969.8068    595296.01   -594869.39    563.16684    55742.797    255.16077     1.393322 
    1950    22.701752    3228.1804    2084.1556    190.74048    1144.0248    232.43889    1247.3333    216.54358            0   -981.18306    595298.59    -594869.7   -309.06733    55742.797    261.65433    1.4460719 
    2000    23.402514    3297.5065    2091.6171    191.42335    1205.8894    238.75396     1287.293    220.47084            0   -968.78447    595297.97   -594869.81    128.84944    55742.797    262.59803    1.4363623 
Loop time of 23.4026 on 4 procs for 2000 steps with 4500 atoms

Performance: 3.692 ns/day, 6.501 hours/ns, 85.461 timesteps/s
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 12.545     | 13.094     | 13.896     |  14.0 | 55.95
Bond    | 0.83177    | 0.90776    | 0.96459    |   5.1 |  3.88
Kspace  | 6.3904     | 7.1918     | 7.7297     |  18.8 | 30.73
Neigh   | 0.38941    | 0.38974    | 0.38988    |   0.0 |  1.67
Comm    | 0.65148    | 0.70795    | 0.7821     |   5.6 |  3.03
Output  | 0.0028274  | 0.0036304  | 0.0057163  |   2.0 |  0.02
Modify  | 1.0483     | 1.0571     | 1.0693     |   0.9 |  4.52
Other   |            | 0.05109    |            |       |  0.22

Nlocal:    1125 ave 1207 max 1003 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost:    5763 ave 5904 max 5656 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs:    214633 ave 220347 max 204542 min
Histogram: 1 0 0 0 0 0 1 0 1 1

Total # of neighbors = 858532
Ave neighs/atom = 190.785
Ave special neighs/atom = 13.3333
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:23
